# Listeria monocytogenes non-coding RNA

Listeria monocytogenes is a gram positive bacterium and causes many food-borne infections such as Listeriosis. This bacteria is ubiquitous in the environment where it can act as either a saprophyte when free living within the environment or as a pathogen when entering a host organism. Many non-coding RNAs have been identified within the bacteria genome where several of these have been classified as novel non-coding RNAs and may contribute to pathogenesis.
Tiling arrays and mutagenesis identified many non-coding RNAs within the L. monocytogenes genome and the location of these non-coding RNAs within the bacterial genome was confirmed by RACE (rapid amplification of cDNA ends) analysis. These studies showed that the expression of many non-coding RNAs was dependent on the environment and that several of these non-coding RNAs act as cis-regulatory elements. Comparisons between previously characterized non-coding RNAs and those present in the L. monocyotogenes genome identified 50 novel non-coding RNAs in L. monocyotogenes. An additional comparative study between the pathogenic L. monocytogenes strain and the non pathogenic L. innocua strain identified several non-coding RNAs that are only present within L. monocytogenes which suggests that these ncRNAs may have a role in pathogenesis. The tables below summarizes the location, flanking genes and also the characteristics of the novel small non-coding RNAs identified and the previously characterized non-coding RNAs present in L. monocytogenes

## Novel Non-coding RNAs

| ID | Start | Stop | Size | 5′ flanking gene | sense of the gene on the genome | $^a$ | | 3′ flanking gene | Characteristic |
| rli22 | 31997 | 32107 | 110 | lmo0028 | -> | -> | -> | lmo0029 | sRNA |
| rli23 | 172171 | 172268 | 97 | lmo0172 | <- | -> | | | sRNA Antisense to lmo0172 transposase Homolog of rli25 and rli35. |
| rli24 | 271029 | 271186 | 157 | lmo0256 | -> | -> | -> | lmo0257 | sRNA |
| rli25 | 357618 | 357516 | 102 | lmo0330 | -> | <- | | | sRNA Antisense to lmo0330: transposase. Homolog of rli23 and rli35 |
| rli26 | 388707 | 388520 | 187 | lmo0360 | -> | <- | <- | lmo0361 | sRNA |
| rli27 | 434831 | 434929 | 98 | lmo0411 | <- | -> | <- | lmo0412 | sRNA |
| rli28 | 507394 | 507206 | 188 | lmo0470 | -> | <- | -> | lmo0471 | sRNA Homolog of rli50 |
| rli29 | 507643 | 507450 | 193 | lmo0470 | -> | <- | -> | lmo0471 | sRNA Antisense to the 5'UTR of lmo0471 |
| rli30 | 540785 | 540670 | 115 | lmo0506 | -> | <- | | | sRNA Antisense to lmo0506 |
| rli31 | 597812 | 597926 | 114 | lmo0558 | <- | -> | -> | lmo0559 | Required for lysozyme resistance and pathogenesis. Structure characterized as two long hairpins. Interacts with the RNA binding global regulator SpoVG. |
| rli32 | 600750 | 600604 | 147 | lmo0560 | <- | <- | <- | lmo0561 | sRNA |
| rli33 | 708326 | 708860 | 534 | lmo0671 | -> | -> | -> | lmo0672 | sRNA |
| rli34 | 803031 | 802948 | 83 | lmo0777 | -> | <- | -> | lmo0778 | sRNA |
| rli35 | 855495 | 855393 | 102 | lmo0828 | -> | <- | | | sRNA Antisense to lmo0828: transposase. Homolog of rli23 and rli25 |
| rli36 | 859527 | 859444 | 83 | nifJ | -> | <- | <- | fbp | sRNA |
| rli37 | 907576 | 907832 | 256 | lmo0866 | -> | -> | -> | lmo0867 | ORF ORF of 58aa. RBS region: TGATACGGGAGTGTGGTGCTAGTTATG |
| rli38 | 1152549 | 1152917 | 369 | lmo1115 | <- | -> | -> | lmo1116 | sRNA role in virulence |
| rli39 | 1179807 | 1179993 | 187 | lmo1149 | -> | -> | <- | lmo1150 | sRNA Annotated as a cobalamin riboswitch in Rfam |
| rli40 | 1275810 | 1275547 | 264 | lmo1251 | -> | <- | <- | lmo1252 | ORF ORF of 64 aa. RBS region: AGTGAGGCGTCCTTATG |
| rli41 | 1277207 | 1276713 | 495 | lmo1252 | <- | <- | -> | lmo1253 | Two ORFs ORF of 45 aa. RBS region: AGAGGAGGTATTTTCTATG ORF of 35 aa. RBS region:AAGGAGGAAAACAAATTG |
| rli42 | 1399617 | 1399447 | 171 | lmo1374 | -> | <- | -> | lmo1375 | sRNA |
| rli43 | 1861630 | 1861377 | 253 | inlC | <- | <- | <- | rplS | ORF ORF of 35aa. RBS region: AGAGTGAGGTGTAATATG |
| rli44 | 2039087 | 2039375 | 289 | lmo1964 | <- | -> | <- | lmo1965 | ORF ORF of 28aa. RBS region: GGAAAGGATAACCCATG |
| rli45 | 2154775 | 2154852 | 77 | lmo2074 | -> | -> | <- | lmo2075 | sRNA Antisense to rli46 |
| rli46 | 2155058 | 2154765 | 294 | lmo2074 | -> | <- | <- | lmo2075 | sRNA Antisense to rli45 |
| rli47 | 2226024 | 2226532 | 508 | lmo2141 | -> | -> | <- | lmo2142 | sRNA |
| rli48 | 2361423 | 2361274 | 149 | lmo2271 | <- | <- | -> | lmo2272 | sRNA |
| rli49 | 2660179 | 2660364 | 185 | lmo2579 | -> | -> | <- | lmo2580 | sRNA |
| rli50 | 2783274 | 2783098 | 176 | lmo2709 | -> | <- | <- | lmo2710 | sRNA Homolog of rli28 |
| rli51 | 207589 | 207709 | 120 | hly | -> | -> | -> | mpl | 5′-UTR-derived Increased in intestinal lumen |
| rli52 | 552421 | 552327 | 94 | lmo0517 | <- | <- | <- | lmo0518 | 5′-UTR-derived Putative riboswitch. |
| rli53 | 955829 | 956001 | 172 | lmo0918 | -> | -> | -> | lmo0919 | 5′-UTR-derived Putative riboswitch. |
| rli54 | 1078584 | 1079111 | 527 | lmo1051 | <- | -> | -> | pdhA | 5′-UTR-derived Putative riboswitch. |
| rli55 | 1198107 | 1198389 | 282 | lmo1170 | -> | -> | -> | pduQ | 5′-UTR-derived Putative riboswitch. |
| rli56 | 1199859 | 1199958 | 99 | pduQ | -> | -> | -> | lmo1172 | 5′-UTR-derived Putative riboswitch. |
| rli57 | ? | 1216658 | ? | lmo1190 | -> | -> | -> | cbiA | 3′-UTR-derived Annotated as a cobalamin riboswitch in Rfam lmo1190-rli57 transcript levelncreasedinintestinal lumen |
| rli58 | ? | 1639974 | ? | rpsD | -> | <- | <- | lmo1597 | |
| rli59 | 1702553 | 1702373 | 180 | lmo1652 | <- | <- | <- | lmo1653 | 5′-UTR-derived |
| rli60 | 2054124 | 2054308 | 184 | lmo1982 | <- | -> | -> | ilvD | 5′-UTR-derived Putative riboswitch. |
| rli61 | 2275363 | 2275258 | 106 | lmo2187 | <- | <- | <- | lmo2188 | 5′-UTR-derived Putative riboswitch |
| rli62 | 2364508 | 2364337 | 172 | lmo2277 | <- | <- | <- | lmo2278 | 5′-UTR-derived Putative riboswitch. |
| rli63 | 2613301 | ? | ? | atpI | <- | <- | <- | lmo2537 | 5′-UTR-derived Putative riboswitch |
| rliA | 513584 | 513807 | 224 | lmo0476 | <- | >- | >- | lmo0477 | snRNA |
| rliB | 544357 | 544716 | 360 | lmo0509 | -> | -> | -> | lmo0510 | sRNA |
| rliC | 1154309 | 1154671 | 363 | lmo1117 | -> | -> | <- | lmo1118 | sRNA |
| rliD | 1359529 | 1359202 | 328 | rpsO | -> | <- | -> | pnpA | sRNA antisense |
| rliE | 1584586 | 1584808 | 223 | comC | <- | -> | <- | folC | sRNA antisense to comC mRNA |
| rliF | 2106292 | 2106073 | 220 | nadA | -> | <- | <- | lmo2026 | snRNA |
| rliG | 2386992 | 2386715 | 278 | lmo2302 | <- | <- | <- | lmo2303 | sRNA |
| rliH | 1180826 | 1181254 | 429 | lmo1150 | <- | -> | -> | lmo1151 | sRNA antisense |
| rliI | 2842200 | 2841962 | 239 | lmo2760 | <- | <- | -> | lmo2761 | sRNA |
| sbrA | 1399363 | 1399433 | 70 | lmo1374 | -> | -> | -> | lmo1375 | sRNA |
$^a$Arrows indicate the sense of the gene on the genome. Bold arrows indicate gene absent from L. innocua.
Listeria monocytogenes EGD-e strain was used in these studies EMBL accession AL591824.1

## Characterised non-coding RNAs

| ID | Rfam |
| SAM | RF00162 |
| LhrC | RF00616 |
| TPP | RF00059 |
| glmS | RF00234 |
| PreQ1 | RF00522 |
| T-box | RF00230 |
| SsrS | RF00013 |
| ID | Rfam |
| LhrB | RF00558 |
| FMN | RF00050 |
| ssrA | RF00023 |
| SRP | RF00169 |
| PrfA | RF00038 |
| L10 leader | RF00557 |
| Purine | RF00167 |
| ID | Rfam |
| lysine | RF00168 |
| yybP-ykoY | RF00080 |
| glycine | RF00504 |
| L21 | RF00559 |
| RyrR | RF00515 |
| LhrA | RF00615 |
| L13 | RF00555 |